These resources will help you set up a strong security policy for your iSeries server.
AS/400 Tips and Tools for Securing your AS/400, SC41-5300 
This book provides a set of practical suggestions for using the security features of iSeries and for establishing operating procedures that are security-conscious.
OS/400 Security Reference, SC41-5302
This book provides information about planning, setting up, managing, and auditing security on your iSeries system. It describes all the features of security on the system and discusses how security features relate to other aspects of the system, such as work management, backup and recovery, and application design.
WebSphere Application Server Version 5 Security
This IBM Redbook provides an overview of WebSphere Application Server Version 5 Security, including J2EE security and programmatic security techniques. It also provides information about end-to-end security solutions that include WebSphere Application Server Version 5 as part of an e-business solution.
AS/400
Internet Security: Protecting Your AS/400 from HARM in the Internet, SG24-4929-00
This document describes all you need to know about iSeries security and how the different security elements fit together. This will help you understand the comprehensive iSeries security options available to secure your system and data.
Domino and WebSphere Integration on the IBM eServer iSeries Server, SG24-6223-00
This IBM Redbook documents the setup and configuration of an integrated environment with WebSphere and Domino on the IBM iSeries server. Part 1 of this redbook focuses on administration topics, such as single signon and the use of a common LDAP directory for authentication, as well as options for different HTTP stacks. Part 2 of this redbook focuses on investigating the application development topic of how WebSphere can access Domino applications. It shows and discusses code snippets from example programs.
HTTP Server (powered by Apache): An Integrated Solution for IBM iSeries Servers, SG24-6716-00
This IBM Redbook is designed to help you plan, install, configure, troubleshoot, and understand the HTTP Server (powered by Apache) running on the IBM iSeries server. It includes configuring the HTTP server for basic authentication, access control and SSL. It also walks you through the steps to implement Web application serving with Java featuring WebSphere Application Server.
iSeries Information Center (V5R2)
Digital certificate management
Digital Certificate Manager (DCM) is a free iSeries feature, to centrally manage certificates for your applications
IBM HTTP Server for iSeries
Information for this topic applies to HTTP Server (powered by Apache)
Security and Directory Services
Read this information to understand iSeries(TM) e-business security and Directory Services offerings
iSeries Information Center (V5R3)
Digital certificate management
Digital Certificate Manager (DCM) is a free iSeries feature, to centrally manage certificates for your applications
IBM HTTP Server for iSeries
Information for this topic applies to HTTP Server (powered by Apache)
Security and Directory Services
Read this information to understand iSeriesTM e-business security and Directory Services offerings